Two new indole diketopiperazine alkaloids (IDAs), (+)19‐epi‐sclerotiamide (1) and (−)19‐epi‐sclerotiamide (2), along with 13 known analogs (3–15), were isolated from a soft coral‐associated epiphytic fungus Aspergillus versicolor CGF 9‐1‐2. The structures of two new compounds were established based on the combination of HR‐ESI‐MS, 1D and 2D NMR spectroscopy, optical rotation measurements and quantum chemical 13C‐NMR, the absolute configurations were determined by experimental and electronic circular dichroism (ECD) calculations. The results of molecular docking showed that all the compounds had a good binding with TDP1, TDP2, TOP1, TOP2, Ache, NLRP3, EGFR, EGFR L858R, EGFR T790M and EGFR T790/L858. Biological evaluation of compounds 3, 6, 8, 11 showed that 3 exerted a strong inhibitory effect on TDP2 with a rate of 81.72 %.